Multi-dimensional characterization of striatal projection neuron heterogeneity in the adult striatum

by Jenesis Gayden, Stephanie Puig, Chaitanya Srinivasan, BaDoi N. Phan, Ghada Abdelhady, Silas A. Buck, Mackenzie C. Gamble, Hugo A. Tejeda, Yan Dong, Andreas R. Pfenning, Ryan W. Logan, Zachary Freyberg*

*Corresponding author:
Zachary Freyberg, M.D., Ph.D.
3811 O’Hara Street, BST W1640
Pittsburgh, PA 15213
Tel: (412) 648-0033
Email: freyberg at pitt dot edu

Link to paper

Multi-species integration of single cell striatal projection neurons

This repository includes the code for comparative integrative analyses of single cell datasets of the mammalian striatum.

The main R-scripts to perform the integration and marker gene analyses are include in the code/ directory.

• step0_*.R: performs dataset specific manipulations to subset data if not already down to striatal projection neurons based on original publication labels
• step1_integrate_multispecies_striatum.ARC.R: performs Seurat reciprocal PCA integration of the SCTransform normalized counts from snRNA-seq and snATAC-seq data in a guided manner
• step2_compute_species_specific_marker_genes.R: calculates dataset conserved marker genes across the subset of snRNA-seq datasets for cell types and subtypes

The scripts to generate the main and supplemental figures are included in the figures/ directory.

• plot_multispecies_integration.R: plots the UMAP and marker gene plots for the main and supplemental figures
• plot_multispecies_proportions.R: calculates the and plots the cell type proportions across striatal subregions